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| Status |
Public on Apr 27, 2022 |
| Title |
control |
| Sample type |
SRA |
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| Source name |
piglet jejunum tissue
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| Organism |
Sus scrofa |
| Characteristics |
age: 5 days old
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification.
RNA libraries were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
one control jejunum sample from the non infected piglet
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| Data processing |
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
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| Submission date |
May 24, 2021 |
| Last update date |
Apr 27, 2022 |
| Contact name |
shi song |
| E-mail(s) |
song.shi@oebiotech.com
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| Organization name |
Shanghai OE Biotech Co., Ltd
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| Street address |
1
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201104 |
| Country |
China |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE175411 |
Identification of cell types and transcriptome landscapes of PEDV infected porcine small intestine using single-cell RNA-sequencing |
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| Relations |
| BioSample |
SAMN19316732 |
| SRA |
SRX10971321 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5333083_control_barcodes.tsv.gz |
34.4 Kb |
(ftp)(http) |
TSV |
| GSM5333083_control_features.tsv.gz |
161.1 Kb |
(ftp)(http) |
TSV |
| GSM5333083_control_matrix.mtx.gz |
41.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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